Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004702.1 Hibiscus syriacus cultivar Beakdansim tig00010567_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 103974
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:494 original size:25 final size:25
Alignment explanation
Indices: 426--542 Score: 114
Period size: 25 Copynumber: 4.7 Consensus size: 25
416 ATTATTAAAA
* * *
426 AATTAATATTAACCATTATTAACAC
1 AATTAATGTTAACAATTACTAACAC
*
451 AA-TAATATT-ACTAATTTACTAACAC
1 AATTAATGTTAAC-AA-TTACTAACAC
* *
476 AATTAATGTTAACCATTACTGACAC
1 AATTAATGTTAACAATTACTAACAC
* *
501 AATTAATGCTAACAATTACTACCAC
1 AATTAATGTTAACAATTACTAACAC
*
526 AATTAATGCT-ACAATTA
1 AATTAATGTTAACAATTA
543 AAATTAACAA
Statistics
Matches: 79, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
23 2 0.03
24 15 0.19
25 53 0.67
26 7 0.09
27 2 0.03
ACGTcount: A:0.45, C:0.18, G:0.03, T:0.33
Consensus pattern (25 bp):
AATTAATGTTAACAATTACTAACAC
Found at i:520 original size:50 final size:50
Alignment explanation
Indices: 426--533 Score: 130
Period size: 50 Copynumber: 2.2 Consensus size: 50
416 ATTATTAAAA
* * *
426 AATTAATATTAACCATTATTAACACAATAATATTACTAATTTACTAACAC
1 AATTAATGTTAACCATTACTAACACAATAATATAACTAATTTACTAACAC
* * *
476 AATTAATGTTAACCATTACTGACACAATTAATGCTAAC-AA-TTACTACCAC
1 AATTAATGTTAACCATTACTAACACAA-TAAT-ATAACTAATTTACTAACAC
526 AATTAATG
1 AATTAATG
534 CTACAATTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
50 41 0.82
51 6 0.12
52 3 0.06
ACGTcount: A:0.45, C:0.18, G:0.04, T:0.33
Consensus pattern (50 bp):
AATTAATGTTAACCATTACTAACACAATAATATAACTAATTTACTAACAC
Found at i:539 original size:12 final size:12
Alignment explanation
Indices: 499--543 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
489 CATTACTGAC
499 ACAATTAATGCT
1 ACAATTAATGCT
* * *
511 AACAATTACTACC
1 -ACAATTAATGCT
524 ACAATTAATGCT
1 ACAATTAATGCT
536 ACAATTAA
1 ACAATTAA
544 AATTAACAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
12 17 0.65
13 9 0.35
ACGTcount: A:0.47, C:0.20, G:0.04, T:0.29
Consensus pattern (12 bp):
ACAATTAATGCT
Found at i:4114 original size:19 final size:20
Alignment explanation
Indices: 4090--4168 Score: 63
Period size: 19 Copynumber: 3.9 Consensus size: 20
4080 CCAGAACCCC
*
4090 AGGGGGTATCGATTCCCCT-
1 AGGGGGAATCGATTCCCCTA
*
4109 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGATTCCCC-T--A
*
4132 AGGGGGAATCGGTT-CCCTCA
1 AGGGGGAATCGATTCCCCT-A
* *
4152 TGGGGGTATCGATTCCC
1 AGGGGGAATCGATTCCC
4169 TCTGCACAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
19 16 0.33
20 13 0.27
21 3 0.06
22 3 0.06
23 14 0.29
ACGTcount: A:0.18, C:0.25, G:0.33, T:0.24
Consensus pattern (20 bp):
AGGGGGAATCGATTCCCCTA
Found at i:4162 original size:20 final size:20
Alignment explanation
Indices: 4091--4170 Score: 65
Period size: 20 Copynumber: 3.9 Consensus size: 20
4081 CAGAACCCCA
*
4091 GGGGGTATCGATTCCC-C-T
1 GGGGGAATCGATTCCCTCAT
* *
4109 AGGGGGAATCGGTTCCCCTTCAAA
1 -GGGGGAATCGATT-CCC-TC-AT
*
4133 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
4153 GGGGGTATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
4171 TGCACAAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
19 11 0.22
20 20 0.40
21 2 0.04
22 4 0.08
23 13 0.26
ACGTcount: A:0.16, C:0.26, G:0.33, T:0.25
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:11488 original size:220 final size:218
Alignment explanation
Indices: 11094--11568 Score: 562
Period size: 220 Copynumber: 2.2 Consensus size: 218
11084 TAAATTCGAA
* * * * * *
11094 GATGACATTGCTCATTCGTGTTGAGGAGATCTAGTCAATGGACGACATTTTCCTTTGTGTTGAGG
1 GATGACATTGCTCATTCGTGTTGAGGAGATCTGGTCAATAGACGACATGTTCCTTCGTATTAAGG
* * * * *
11159 ACTTCTAGCCGTATTTGTTAATTACGCAAGTGGAGACAATGATGTTTCTTCGAGTTGAGGAAGTC
66 ACTTCTAGCCGTATTTGGTAATAACGCAAGTGGAGACAATGATGTTCCTCCGAGTTGAGAAAGTC
* * *
11224 TAGTTGTCCTTAGATTACTTGATTTGAAAATGAAACAACTCCTACGTGATGAGGAGATCGAGTCA
131 TAGCTGTCCTTAGATTACTTGAATTGAAAATGAAACAACTCCTACGTGATGAAGAGATCGAGTCA
* * * * *
11289 TTTTTCTTGATGTTAAGTCTGAT
196 TTTTGCTTAATATCAAATCTGAT
*
11312 GATGACATTGCTTC-TTCGTGTTGAGGAGATATGGTCAATAGACGACATCGTTCCTTCGTATTAA
1 GATGACATTGC-TCATTCGTGTTGAGGAGATCTGGTCAATAGACGACAT-GTTCCTTCGTATTAA
* * * ** * * * *
11376 GGTCGTT-TAGTCGTATTTGGGTAATAATGCAAGTGGAGATGATGTTGTTCCTCCGCGTTTATAA
64 GGAC-TTCTAGCCGTATTT-GGTAATAACGCAAGTGGAGACAATGATGTTCCTCCGAGTTGAGAA
* *
11440 AGTCT-GACTGT-CTATAGATTACTTGAATTGAAAATGACACAGCTCCTACGTGATGAAGAGATC
127 AGTCTAG-CTGTCCT-TAGATTACTTGAATTGAAAATGAAACAACTCCTACGTGATGAAGAGATC
*
11503 GGGTCATTTTGCTTAATATCAAATCTGAT
190 GAGTCATTTTGCTTAATATCAAATCTGAT
* *
11532 GATGACACTGCTCATTCGTATTGAGGAGATCTGGTCA
1 GATGACATTGCTCATTCGTGTTGAGGAGATCTGGTCA
11569 TAGTTGAAAG
Statistics
Matches: 215, Mismatches: 35, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
218 42 0.20
219 31 0.14
220 142 0.66
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (218 bp):
GATGACATTGCTCATTCGTGTTGAGGAGATCTGGTCAATAGACGACATGTTCCTTCGTATTAAGG
ACTTCTAGCCGTATTTGGTAATAACGCAAGTGGAGACAATGATGTTCCTCCGAGTTGAGAAAGTC
TAGCTGTCCTTAGATTACTTGAATTGAAAATGAAACAACTCCTACGTGATGAAGAGATCGAGTCA
TTTTGCTTAATATCAAATCTGAT
Found at i:12590 original size:12 final size:12
Alignment explanation
Indices: 12575--12609 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
12565 AAGAAAACCA
12575 AAAGAAAAACTT
1 AAAGAAAAACTT
12587 AAAG-AAAACTT
1 AAAGAAAAACTT
*
12598 AATGAAAAACTT
1 AAAGAAAAACTT
12610 GATGTAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.63, C:0.09, G:0.09, T:0.20
Consensus pattern (12 bp):
AAAGAAAAACTT
Found at i:12618 original size:12 final size:12
Alignment explanation
Indices: 12578--12624 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
12568 AAAACCAAAA
*
12578 GAAAAACTTAAA
1 GAAAAACTTAAT
12590 G-AAAACTTAAT
1 GAAAAACTTAAT
*
12601 GAAAAACTTGAT
1 GAAAAACTTAAT
*
12613 GTAAAAC-TAAT
1 GAAAAACTTAAT
12624 G
1 G
12625 CCTCCTATGA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 14 0.47
12 16 0.53
ACGTcount: A:0.55, C:0.09, G:0.13, T:0.23
Consensus pattern (12 bp):
GAAAAACTTAAT
Found at i:12624 original size:23 final size:23
Alignment explanation
Indices: 12564--12609 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
12554 CTCATAATTG
** *
12564 AAAGAAAACCAAAAGAAAAACTT
1 AAAGAAAACTTAATGAAAAACTT
12587 AAAGAAAACTTAATGAAAAACTT
1 AAAGAAAACTTAATGAAAAACTT
12610 GATGTAAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.65, C:0.11, G:0.09, T:0.15
Consensus pattern (23 bp):
AAAGAAAACTTAATGAAAAACTT
Found at i:16938 original size:20 final size:20
Alignment explanation
Indices: 16902--16939 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
16892 TTTTGGTGCA
*
16902 GAGGGAATCGATACCCCCAT
1 GAGGGAATCAATACCCCCAT
*
16922 GAGGGAATCAATTCCCCC
1 GAGGGAATCAATACCCCC
16940 TTTGAAGGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.32, G:0.24, T:0.16
Consensus pattern (20 bp):
GAGGGAATCAATACCCCCAT
Found at i:20402 original size:17 final size:16
Alignment explanation
Indices: 20382--20420 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
20372 AAAATCAAGG
20382 AAAAATAAAATAAAAAT
1 AAAAAT-AAATAAAAAT
20399 AAAAATAAATAAAAAT
1 AAAAATAAATAAAAAT
*
20415 AGAAAT
1 AAAAAT
20421 TGAAAAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (16 bp):
AAAAATAAATAAAAAT
Found at i:21775 original size:102 final size:102
Alignment explanation
Indices: 21657--21865 Score: 276
Period size: 102 Copynumber: 2.0 Consensus size: 102
21647 CAAGAATTTC
** *
21657 TTTCTCTTCTGTTTCTTTCTTAGACTTAGCGAATCTAGAGAGAAAAGGAGGATATATGAAAAATT
1 TTTCTCTTCTACTTCTTTCTTAGACTTAGCGAATCTAGAGAGAAAAGGAAGATATATGAAAAATT
* **
21722 CCTTC-AGTTTTTCACTTTTGAGTTTTTTAGGTTGGTA
66 CCTTCGA-TTTTTCACTTTTGAATCCTTTAGGTTGGTA
* * * * * *
21759 TTTCTCTTCTACTTCTTTCTTGGACTTGGCGAATCTAGAGGGAAAATGAAGATCTATGACAAATT
1 TTTCTCTTCTACTTCTTTCTTAGACTTAGCGAATCTAGAGAGAAAAGGAAGATATATGAAAAATT
* *
21824 CCTTCGATTTTTCGCTTTTGAATCCTTTAGGTTGGTC
66 CCTTCGATTTTTCACTTTTGAATCCTTTAGGTTGGTA
21861 TTTCT
1 TTTCT
21866 GAGTCTGAAG
Statistics
Matches: 92, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
102 91 0.99
103 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (102 bp):
TTTCTCTTCTACTTCTTTCTTAGACTTAGCGAATCTAGAGAGAAAAGGAAGATATATGAAAAATT
CCTTCGATTTTTCACTTTTGAATCCTTTAGGTTGGTA
Found at i:24183 original size:12 final size:12
Alignment explanation
Indices: 24168--24202 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
24158 AAGAAAACCA
24168 AAAGAAAAACTT
1 AAAGAAAAACTT
24180 AAAG-AAAACTT
1 AAAGAAAAACTT
*
24191 AATGAAAAACTT
1 AAAGAAAAACTT
24203 GATGTAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.63, C:0.09, G:0.09, T:0.20
Consensus pattern (12 bp):
AAAGAAAAACTT
Found at i:24211 original size:12 final size:12
Alignment explanation
Indices: 24171--24217 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
24161 AAAACCAAAA
*
24171 GAAAAACTTAAA
1 GAAAAACTTAAT
24183 G-AAAACTTAAT
1 GAAAAACTTAAT
*
24194 GAAAAACTTGAT
1 GAAAAACTTAAT
*
24206 GTAAAAC-TAAT
1 GAAAAACTTAAT
24217 G
1 G
24218 CCTCCTATGA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 14 0.47
12 16 0.53
ACGTcount: A:0.55, C:0.09, G:0.13, T:0.23
Consensus pattern (12 bp):
GAAAAACTTAAT
Found at i:24217 original size:23 final size:23
Alignment explanation
Indices: 24157--24202 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
24147 CTCATAATTG
** *
24157 AAAGAAAACCAAAAGAAAAACTT
1 AAAGAAAACTTAATGAAAAACTT
24180 AAAGAAAACTTAATGAAAAACTT
1 AAAGAAAACTTAATGAAAAACTT
24203 GATGTAAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.65, C:0.11, G:0.09, T:0.15
Consensus pattern (23 bp):
AAAGAAAACTTAATGAAAAACTT
Found at i:24797 original size:3 final size:3
Alignment explanation
Indices: 24784--24829 Score: 56
Period size: 3 Copynumber: 14.7 Consensus size: 3
24774 ATATTATAAA
* *
24784 TAT TAAT TAT TAT TAT TAT TAA AAT ATAT TAT TAT TAT TAT TAT TA
1 TAT T-AT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TA
24830 ATACAAATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
3 32 0.86
4 5 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:24802 original size:22 final size:23
Alignment explanation
Indices: 24775--24832 Score: 73
Period size: 25 Copynumber: 2.5 Consensus size: 23
24765 ATTAAAACTA
24775 TATTATAAATAT-TAATTATTAT
1 TATTATAAATATATAATTATTAT
*
24797 TATTATTAAAATATATTATTATTAT
1 TATTA-T-AAATATATAATTATTAT
*
24822 TATTATTAATA
1 TATTATAAATA
24833 CAAATTACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 5 0.16
23 5 0.16
24 7 0.23
25 14 0.45
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTATAAATATATAATTATTAT
Found at i:24813 original size:19 final size:19
Alignment explanation
Indices: 24765--24823 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
24755 TTTAACCGAG
* *
24765 ATTAAAACTATATTATAAAT
1 ATTAAAA-TATATTATTATT
24785 ATT--AAT-TATTATTATT
1 ATTAAAATATATTATTATT
24801 ATTAAAATATATTATTATT
1 ATTAAAATATATTATTATT
24820 ATTA
1 ATTA
24824 TTATTAATAC
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
16 11 0.32
17 1 0.03
18 5 0.15
19 14 0.41
20 3 0.09
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTAAAATATATTATTATT
Found at i:24839 original size:25 final size:25
Alignment explanation
Indices: 24789--24839 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
24779 ATAAATATTA
* *
24789 ATTATTATTATTATTAAAATATATT
1 ATTATTATTATTATTAAAACAAATT
*
24814 ATTATTATTATTATTAATACAAATT
1 ATTATTATTATTATTAAAACAAATT
24839 A
1 A
24840 CATTATTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (25 bp):
ATTATTATTATTATTAAAACAAATT
Found at i:26569 original size:32 final size:32
Alignment explanation
Indices: 26533--26602 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
26523 AAATAATATC
26533 TTTTATATATATATAA-ATATATGATTTCTTTA
1 TTTTATATATATATAATATA-ATGATTTCTTTA
26565 TTTTATATATATATAATATAATGATTTCTTTA
1 TTTTATATATATATAATATAATGATTTCTTTA
26597 TTTTAT
1 TTTTAT
26603 TTTATTTACC
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
32 34 0.92
33 3 0.08
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (32 bp):
TTTTATATATATATAATATAATGATTTCTTTA
Found at i:27912 original size:26 final size:28
Alignment explanation
Indices: 27883--27938 Score: 89
Period size: 26 Copynumber: 2.0 Consensus size: 28
27873 TTGAATCTCA
27883 TTTCATCATTTTTT-TTA-TTTTTCATT
1 TTTCATCATTTTTTATTATTTTTTCATT
27909 TTTCATCATTTTTTCATTATTTTTTCATT
1 TTTCATCATTTTTT-ATTATTTTTTCATT
27938 T
1 T
27939 CATTATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 14 0.52
28 3 0.11
29 10 0.37
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.71
Consensus pattern (28 bp):
TTTCATCATTTTTTATTATTTTTTCATT
Found at i:27950 original size:11 final size:11
Alignment explanation
Indices: 27907--27937 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
27897 TTATTTTTCA
*
27907 TTTTTCATCAT
1 TTTTTCATTAT
27918 TTTTTCATTAT
1 TTTTTCATTAT
27929 TTTTTCATT
1 TTTTTCATT
27938 TCATTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.16, C:0.13, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTTTCATTAT
Found at i:27955 original size:19 final size:16
Alignment explanation
Indices: 27920--27950 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
27910 TTCATCATTT
27920 TTTCATTATTTTTTCA
1 TTTCATTATTTTTTCA
27936 TTTCATTATTTTTTC
1 TTTCATTATTTTTTC
27951 TTCATATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.13, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTCATTATTTTTTCA
Found at i:47258 original size:32 final size:32
Alignment explanation
Indices: 47221--47304 Score: 114
Period size: 32 Copynumber: 2.6 Consensus size: 32
47211 AGATATTGGT
* *
47221 AGTGTTGCATTCAGATAATGCATAACAGAGTC
1 AGTGTTGCATTTAGATAATGCACAACAGAGTC
* * *
47253 AGTGTTGCATTTAGATAATGCACAAGAGTGTT
1 AGTGTTGCATTTAGATAATGCACAACAGAGTC
*
47285 AGTATTGCATTTAGATAATG
1 AGTGTTGCATTTAGATAATG
47305 TGTAGCAGTT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (32 bp):
AGTGTTGCATTTAGATAATGCACAACAGAGTC
Found at i:47803 original size:38 final size:38
Alignment explanation
Indices: 47752--47828 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
47742 TTTCATCATT
*
47752 TCGTTTGATACATTAAACTTGCATAATTAACTTGGGTA
1 TCGTTTGATACATTAAACTTACATAATTAACTTGGGTA
*
47790 TCGTTTGATACATTAAACTTACATAATTAAGTTGGGTA
1 TCGTTTGATACATTAAACTTACATAATTAACTTGGGTA
47828 T
1 T
47829 ATATATGGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (38 bp):
TCGTTTGATACATTAAACTTACATAATTAACTTGGGTA
Found at i:48128 original size:13 final size:14
Alignment explanation
Indices: 48104--48132 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
48094 TTAATTAATG
48104 ATTATAAATATATT
1 ATTATAAATATATT
48118 ATTAT-AATATATT
1 ATTATAAATATATT
48131 AT
1 AT
48133 GTTAACTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTATAAATATATT
Found at i:48797 original size:21 final size:21
Alignment explanation
Indices: 48747--48798 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
48737 AAATTTTATT
*
48747 TATTTTTAAATAATTAAAATA
1 TATTTTAAAATAATTAAAATA
* *
48768 AATTATTAAAAGTAA-TAAATTA
1 TATT-TTAAAA-TAATTAAAATA
48790 TATTTTAAA
1 TATTTTAAA
48799 GATGTTAGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 8 0.32
22 14 0.56
23 3 0.12
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
TATTTTAAAATAATTAAAATA
Found at i:50992 original size:35 final size:35
Alignment explanation
Indices: 50919--50993 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
50909 CGTCACTAAC
**
50919 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
50954 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
50989 AGTAA
1 AGTAA
50994 TCTTCCTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.29, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:51130 original size:23 final size:23
Alignment explanation
Indices: 51070--51144 Score: 105
Period size: 24 Copynumber: 3.2 Consensus size: 23
51060 CATAATTCAA
*
51070 GTCAAGTATCATATCAGAATCCAG
1 GTCAA-TATCAGATCAGAATCCAG
* *
51094 GTCATGTATCAGATCAGAATCCAT
1 GTCA-ATATCAGATCAGAATCCAG
51118 GTCAATATCAGATCAGAATCCAG
1 GTCAATATCAGATCAGAATCCAG
51141 GTCA
1 GTCA
51145 GGATCATAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
23 21 0.47
24 24 0.53
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.25
Consensus pattern (23 bp):
GTCAATATCAGATCAGAATCCAG
Found at i:51150 original size:23 final size:23
Alignment explanation
Indices: 51074--51159 Score: 109
Period size: 23 Copynumber: 3.7 Consensus size: 23
51064 ATTCAAGTCA
*
51074 AGTATCATATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
*
51097 ATGTATCAGATCAGAATCCATGTC
1 A-GTATCAGATCAGAATCCAGGTC
*
51121 AATATCAGATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
* * *
51144 AGGATCATAACAGAAT
1 AGTATCAGATCAGAAT
51160 TCAAGTCGGA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
23 33 0.61
24 21 0.39
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.24
Consensus pattern (23 bp):
AGTATCAGATCAGAATCCAGGTC
Found at i:51177 original size:47 final size:47
Alignment explanation
Indices: 51053--51166 Score: 131
Period size: 47 Copynumber: 2.4 Consensus size: 47
51043 TATATCAAAA
* * * * *
51053 ATCAAAACATAATTCAAGTCAAGTATCATATCAGAATCCAGGTCATGT
1 ATCAGAACAGAATCCAAGTCAA-TATCAGATCAGAATCCAGGTCATGG
* *
51101 ATCAGATCAGAATCCATGTCAATATCAGATCAGAATCCAGGTCA-GG
1 ATCAGAACAGAATCCAAGTCAATATCAGATCAGAATCCAGGTCATGG
* *
51147 ATCATAACAGAATTCAAGTC
1 ATCAGAACAGAATCCAAGTC
51167 GGAAATCAGA
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
46 17 0.31
47 21 0.38
48 17 0.31
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (47 bp):
ATCAGAACAGAATCCAAGTCAATATCAGATCAGAATCCAGGTCATGG
Found at i:52325 original size:18 final size:18
Alignment explanation
Indices: 52304--52339 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
52294 CTTCCATCCG
*
52304 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
52322 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
52340 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:53663 original size:7 final size:7
Alignment explanation
Indices: 53651--53682 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
53641 TGGTCAACTC
53651 CGGTCAA
1 CGGTCAA
53658 CGGTCAA
1 CGGTCAA
53665 CGGGTCAA
1 C-GGTCAA
53673 CGGTCAA
1 CGGTCAA
53680 CGG
1 CGG
53683 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:53672 original size:8 final size:8
Alignment explanation
Indices: 53652--53698 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
53642 GGTCAACTCC
53652 GGTCAAC-
1 GGTCAACG
53659 GGTCAACG
1 GGTCAACG
53667 GGTCAAC-
1 GGTCAACG
53674 GGTCAACG
1 GGTCAACG
53682 GGT---CG
1 GGTCAACG
53687 GGTCAACG
1 GGTCAACG
53695 GGTC
1 GGTC
53699 GGGTCGGGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
5 5 0.14
7 14 0.40
8 16 0.46
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:53672 original size:15 final size:15
Alignment explanation
Indices: 53652--53698 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
53642 GGTCAACTCC
53652 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
53667 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
53682 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
53695 GGTC
1 GGTC
53699 GGGTCGGGTG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:53692 original size:13 final size:13
Alignment explanation
Indices: 53659--53703 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
53649 TCCGGTCAAC
*
53659 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
53674 GGTCAACGGGTCG
1 GGTCAACGGGTCG
53687 GGTCAACGGGTCG
1 GGTCAACGGGTCG
53700 GGTC
1 GGTC
53704 GGGTGAACGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 17 0.59
15 12 0.41
ACGTcount: A:0.18, C:0.24, G:0.42, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:53744 original size:18 final size:18
Alignment explanation
Indices: 53680--53744 Score: 112
Period size: 18 Copynumber: 3.6 Consensus size: 18
53670 CAACGGTCAA
*
53680 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTTAACGGGT
*
53698 CGGGTCGGGTGAACGGGT
1 CGGGTCGGGTTAACGGGT
53716 CGGGTCGGGTTAACGGGT
1 CGGGTCGGGTTAACGGGT
53734 CGGGTCGGGTT
1 CGGGTCGGGTT
53745 GTGACCGGTC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.09, C:0.18, G:0.52, T:0.20
Consensus pattern (18 bp):
CGGGTCGGGTTAACGGGT
Found at i:55834 original size:35 final size:35
Alignment explanation
Indices: 55761--55835 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
55751 CGTCACTAAC
**
55761 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
55796 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
55831 AGTAA
1 AGTAA
55836 TCTTCCTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.29, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:55973 original size:23 final size:23
Alignment explanation
Indices: 55913--55987 Score: 105
Period size: 24 Copynumber: 3.2 Consensus size: 23
55903 CATAATTCAA
*
55913 GTCAAGTATCATATCAGAATCCAG
1 GTCAA-TATCAGATCAGAATCCAG
* *
55937 GTCATGTATCAGATCAGAATCCAT
1 GTCA-ATATCAGATCAGAATCCAG
55961 GTCAATATCAGATCAGAATCCAG
1 GTCAATATCAGATCAGAATCCAG
55984 GTCA
1 GTCA
55988 GGATCATAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
23 21 0.47
24 24 0.53
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.25
Consensus pattern (23 bp):
GTCAATATCAGATCAGAATCCAG
Found at i:55993 original size:23 final size:23
Alignment explanation
Indices: 55917--56002 Score: 109
Period size: 23 Copynumber: 3.7 Consensus size: 23
55907 ATTCAAGTCA
*
55917 AGTATCATATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
*
55940 ATGTATCAGATCAGAATCCATGTC
1 A-GTATCAGATCAGAATCCAGGTC
*
55964 AATATCAGATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
* * *
55987 AGGATCATAACAGAAT
1 AGTATCAGATCAGAAT
56003 TCAAGTCGGA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
23 33 0.61
24 21 0.39
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.24
Consensus pattern (23 bp):
AGTATCAGATCAGAATCCAGGTC
Found at i:56020 original size:47 final size:47
Alignment explanation
Indices: 55896--56009 Score: 131
Period size: 47 Copynumber: 2.4 Consensus size: 47
55886 TATATCAAAA
* * * * *
55896 ATCAAAACATAATTCAAGTCAAGTATCATATCAGAATCCAGGTCATGT
1 ATCAGAACAGAATCCAAGTCAA-TATCAGATCAGAATCCAGGTCATGG
* *
55944 ATCAGATCAGAATCCATGTCAATATCAGATCAGAATCCAGGTCA-GG
1 ATCAGAACAGAATCCAAGTCAATATCAGATCAGAATCCAGGTCATGG
* *
55990 ATCATAACAGAATTCAAGTC
1 ATCAGAACAGAATCCAAGTC
56010 GGAAATCAGA
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
46 17 0.31
47 21 0.38
48 17 0.31
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (47 bp):
ATCAGAACAGAATCCAAGTCAATATCAGATCAGAATCCAGGTCATGG
Found at i:57167 original size:18 final size:18
Alignment explanation
Indices: 57146--57181 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
57136 CTTCCATCCG
*
57146 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
57164 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
57182 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:58503 original size:7 final size:7
Alignment explanation
Indices: 58491--58522 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
58481 TGGTCAACTC
58491 CGGTCAA
1 CGGTCAA
58498 CGGTCAA
1 CGGTCAA
58505 CGGGTCAA
1 C-GGTCAA
58513 CGGTCAA
1 CGGTCAA
58520 CGG
1 CGG
58523 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:58512 original size:8 final size:8
Alignment explanation
Indices: 58492--58538 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
58482 GGTCAACTCC
58492 GGTCAAC-
1 GGTCAACG
58499 GGTCAACG
1 GGTCAACG
58507 GGTCAAC-
1 GGTCAACG
58514 GGTCAACG
1 GGTCAACG
58522 GGT---CG
1 GGTCAACG
58527 GGTCAACG
1 GGTCAACG
58535 GGTC
1 GGTC
58539 GGGTCGGGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
5 5 0.14
7 14 0.40
8 16 0.46
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:58512 original size:15 final size:15
Alignment explanation
Indices: 58492--58538 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
58482 GGTCAACTCC
58492 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
58507 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
58522 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
58535 GGTC
1 GGTC
58539 GGGTCGGGTG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:58532 original size:13 final size:13
Alignment explanation
Indices: 58499--58543 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
58489 TCCGGTCAAC
*
58499 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
58514 GGTCAACGGGTCG
1 GGTCAACGGGTCG
58527 GGTCAACGGGTCG
1 GGTCAACGGGTCG
58540 GGTC
1 GGTC
58544 GGGTGAACGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 17 0.59
15 12 0.41
ACGTcount: A:0.18, C:0.24, G:0.42, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:58584 original size:18 final size:18
Alignment explanation
Indices: 58520--58584 Score: 112
Period size: 18 Copynumber: 3.6 Consensus size: 18
58510 CAACGGTCAA
*
58520 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTTAACGGGT
*
58538 CGGGTCGGGTGAACGGGT
1 CGGGTCGGGTTAACGGGT
58556 CGGGTCGGGTTAACGGGT
1 CGGGTCGGGTTAACGGGT
58574 CGGGTCGGGTT
1 CGGGTCGGGTT
58585 GTGACCGGTC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.09, C:0.18, G:0.52, T:0.20
Consensus pattern (18 bp):
CGGGTCGGGTTAACGGGT
Found at i:70437 original size:27 final size:25
Alignment explanation
Indices: 70385--70437 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
70375 ATAAAAATTT
* * *
70385 TAAAAATATGAAATTAGACTATTAA
1 TAAAAATATAAAAATAAACTATTAA
70410 TAAAAATATAAAAAATAAACTATATAA
1 TAAAAATAT-AAAAATAAACTAT-TAA
70437 T
1 T
70438 TTGTTTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 9 0.39
26 10 0.43
27 4 0.17
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (25 bp):
TAAAAATATAAAAATAAACTATTAA
Found at i:70585 original size:17 final size:17
Alignment explanation
Indices: 70563--70627 Score: 51
Period size: 19 Copynumber: 3.6 Consensus size: 17
70553 ATATTTGTAT
70563 AATTTAAAAAATAAGAA
1 AATTTAAAAAATAAGAA
*
70580 AATTTATATAAAA-ATTGAA
1 AATTTA-A-AAAATA-AGAA
*
70599 ATATTTTAAAAAATAACAA
1 A-A-TTTAAAAAATAAGAA
*
70618 AAATTAAAAA
1 AATTTAAAAA
70628 GTGTGGTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
17 13 0.34
18 3 0.08
19 15 0.39
20 3 0.08
21 4 0.11
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (17 bp):
AATTTAAAAAATAAGAA
Found at i:70592 original size:20 final size:18
Alignment explanation
Indices: 70565--70619 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
70555 ATTTGTATAA
70565 TTTAAAAAATAAGAAAAT
1 TTTAAAAAATAAGAAAAT
*
70583 TTATATAAAAAT-TGAAATAT
1 TT-TA-AAAAATAAGAAA-AT
*
70603 TTTAAAAAATAACAAAA
1 TTTAAAAAATAAGAAAA
70620 ATTAAAAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
18 9 0.30
19 11 0.37
20 10 0.33
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.31
Consensus pattern (18 bp):
TTTAAAAAATAAGAAAAT
Found at i:70599 original size:19 final size:18
Alignment explanation
Indices: 70565--70612 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
70555 ATTTGTATAA
*
70565 TTTAAAAAATAAGAAA-AT
1 TTTAAAAAAT-TGAAATAT
70583 TTATATAAAAATTGAAATAT
1 TT-TA-AAAAATTGAAATAT
70603 TTTAAAAAAT
1 TTTAAAAAAT
70613 AACAAAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 8 0.31
19 8 0.31
20 10 0.38
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.35
Consensus pattern (18 bp):
TTTAAAAAATTGAAATAT
Found at i:80420 original size:64 final size:63
Alignment explanation
Indices: 80284--80505 Score: 268
Period size: 64 Copynumber: 3.5 Consensus size: 63
80274 TGTTTAAATG
** **
80284 TGCATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAATAA-ATACATCGAATGCAATTCA
1 TGCATCGATGCATAAGTAGTGCATCGATGCATC-CCATTAATAATATACATCGAATGCAATTCA
*
80346 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTCA
1 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAAT-ATACATCGAATGCAATTCA
** * ** *
80410 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGCAATAATACTACATCGAATACCTTTTA
1 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATA-TACATCGAATGCAATTCA
* * * *
80474 TGTACCGATGTATCAGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAGTAGTGCATCGATGCAT
80506 ACCTTCATTA
Statistics
Matches: 140, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
62 37 0.26
63 2 0.01
64 101 0.72
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (63 bp):
TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATATACATCGAATGCAATTCA
Found at i:80894 original size:27 final size:29
Alignment explanation
Indices: 80846--80917 Score: 123
Period size: 27 Copynumber: 2.6 Consensus size: 29
80836 TGATATGAAG
80846 TGACATGAGCTACATGATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
80875 TGACATGA-CTAC-TGATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
80902 TGACATGAG-TACATGA
1 TGACATGAGCTACATGA
80918 ACATATGAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
27 26 0.63
28 7 0.17
29 8 0.20
ACGTcount: A:0.43, C:0.17, G:0.21, T:0.19
Consensus pattern (29 bp):
TGACATGAGCTACATGATCACAAGAGAAA
Found at i:87325 original size:64 final size:64
Alignment explanation
Indices: 87256--87479 Score: 272
Period size: 64 Copynumber: 3.5 Consensus size: 64
87246 TGTTTGAATG
** ** *
87256 TGCATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATTCAATTC
1 TGCATCGATGCATAAGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAATTC
87319 A
64 A
*
87320 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTCA
1 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
** ** * ** *
87384 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCAACAATAATACTACATCGAATACCTTTTA
1 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
* *
87448 TGCACCGATGCATCAGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAGTAGTGCATCGATGCAT
87480 ACCTTCATTA
Statistics
Matches: 141, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
64 135 0.96
65 6 0.04
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (64 bp):
TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
Found at i:87434 original size:128 final size:128
Alignment explanation
Indices: 87256--87497 Score: 312
Period size: 128 Copynumber: 1.9 Consensus size: 128
87246 TGTTTGAATG
** ** *
87256 TGCATCGATGCATTGGTAGTGCATCGATGCACTCTTTTAAAATAAATACATCGAATTCAATTCAT
1 TGCATCGATGCATAAGTAGTGCATCGATGCACTC-TCCAAAATAAATACATCGAATACAATTCAT
*
87321 GCATCGATGCATAAGTAGTGCATCGATGCAT-CC-CATTAATAATGAAACATCGAATGCAATTCA
65 GCACCGATGCATAAGTAGTGCATCGATGCATACCTCATTAA-AATGAAACATCGAATGCAATTCA
** *
87384 TGCATCGATGCATAAGTAGTGCATCGATGCA-TC-CCAACAATAATACTACATCGAATACCTTTT
1 TGCATCGATGCATAAGTAGTGCATCGATGCACTCTCCAA-AATAA-A-TACATCGAATACAATTC
*
87447 ATGCACCGATGCATCAGTAGTGCATCGATGCATACCTTCATTAAAATGAAA
63 ATGCACCGATGCATAAGTAGTGCATCGATGCATACC-TCATTAAAATGAAA
87498 TTGACTTTTC
Statistics
Matches: 98, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
125 2 0.02
126 5 0.05
127 3 0.03
128 73 0.74
129 2 0.02
130 7 0.07
131 6 0.06
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (128 bp):
TGCATCGATGCATAAGTAGTGCATCGATGCACTCTCCAAAATAAATACATCGAATACAATTCATG
CACCGATGCATAAGTAGTGCATCGATGCATACCTCATTAAAATGAAACATCGAATGCAATTCA
Found at i:87798 original size:24 final size:24
Alignment explanation
Indices: 87771--87818 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
87761 ACATGCATAA
*
87771 GATATAT-ATATGTTCATGTGATAT
1 GATATATGATATG-ACATGTGATAT
*
87795 GATATGTGATATGACATGTGATAT
1 GATATATGATATGACATGTGATAT
87819 AAGAACATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.33, C:0.04, G:0.21, T:0.42
Consensus pattern (24 bp):
GATATATGATATGACATGTGATAT
Found at i:87803 original size:12 final size:12
Alignment explanation
Indices: 87785--87818 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
87775 TATATATGTT
87785 CATGTGATATGA
1 CATGTGATATGA
*
87797 TATGTGATATGA
1 CATGTGATATGA
87809 CATGTGATAT
1 CATGTGATAT
87819 AAGAACATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.38
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:87871 original size:29 final size:29
Alignment explanation
Indices: 87836--87909 Score: 132
Period size: 29 Copynumber: 2.6 Consensus size: 29
87826 TGATATGAAG
87836 TGACATGAGCTACATGATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
*
87865 TGACATGAGCTAAATGATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
87894 TGACATGAG-TACATGA
1 TGACATGAGCTACATGA
87910 ACATATGAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
28 6 0.14
29 37 0.86
ACGTcount: A:0.45, C:0.15, G:0.22, T:0.19
Consensus pattern (29 bp):
TGACATGAGCTACATGATCACAAGAGAAA
Found at i:87896 original size:15 final size:15
Alignment explanation
Indices: 87849--87896 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
87839 CATGAGCTAC
87849 ATGATCACAAGAGAA
1 ATGATCACAAGAGAA
** **
87864 ATGA-CATGAGCTAA
1 ATGATCACAAGAGAA
87878 ATGATCACAAGAGAA
1 ATGATCACAAGAGAA
87893 ATGA
1 ATGA
87897 CATGAGTACA
Statistics
Matches: 24, Mismatches: 8, Indels: 2
0.71 0.24 0.06
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.50, C:0.12, G:0.21, T:0.17
Consensus pattern (15 bp):
ATGATCACAAGAGAA
Found at i:93633 original size:16 final size:16
Alignment explanation
Indices: 93612--93656 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
93602 ATGATTAAGC
*
93612 GCTGAATTATTCAAAT
1 GCTGAATGATTCAAAT
93628 GCTGAATGATTCAAAT
1 GCTGAATGATTCAAAT
93644 GCTGAATGATTCA
1 GCTGAATGATTCA
93657 GAGGCTCTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (16 bp):
GCTGAATGATTCAAAT
Found at i:93746 original size:27 final size:27
Alignment explanation
Indices: 93708--93773 Score: 123
Period size: 27 Copynumber: 2.4 Consensus size: 27
93698 GATAATGGCT
93708 CTGAATCATTCAGAATGTACTTCTGTG
1 CTGAATCATTCAGAATGTACTTCTGTG
*
93735 CTGAATCATTCAGAATGTACTTTTGTG
1 CTGAATCATTCAGAATGTACTTCTGTG
93762 CTGAATCATTCA
1 CTGAATCATTCA
93774 ACACTGTTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (27 bp):
CTGAATCATTCAGAATGTACTTCTGTG
Found at i:96485 original size:46 final size:46
Alignment explanation
Indices: 96435--96528 Score: 102
Period size: 46 Copynumber: 2.0 Consensus size: 46
96425 AATATTTAAA
96435 TTTAAAAACAAATTTTATT-TATTAAAATT-TAAATTAAATTCAATAT
1 TTTAAAAACAAA-TTTATTAT-TTAAAATTCTAAATTAAATTCAATAT
* ** * * *
96481 TTTAATATTAAATTTATTATTTATAGTTCTAAATTAAATTCAGTAT
1 TTTAAAAACAAATTTATTATTTAAAATTCTAAATTAAATTCAATAT
96527 TT
1 TT
96529 GTTTCATATT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
45 12 0.30
46 28 0.70
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (46 bp):
TTTAAAAACAAATTTATTATTTAAAATTCTAAATTAAATTCAATAT
Found at i:96490 original size:32 final size:32
Alignment explanation
Indices: 96428--96496 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 32
96418 TTAGTATAAT
*
96428 ATTTAAATTTAAAAACAAATTTTATTTATTAAA
1 ATTTAAATTTAAAAACAAATTTTATATATT-AA
**
96461 ATTTAAA-TTAAATTCAATATTTTA-ATATTAA
1 ATTTAAATTTAAAAACAA-ATTTTATATATTAA
96492 ATTTA
1 ATTTA
96497 TTATTTATAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 7 0.22
32 12 0.38
33 13 0.41
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (32 bp):
ATTTAAATTTAAAAACAAATTTTATATATTAA
Found at i:97369 original size:2 final size:2
Alignment explanation
Indices: 97362--97416 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
97352 TTAGTTCTAT
97362 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
97403 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
97417 AATGGGTTAG
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:101440 original size:3 final size:3
Alignment explanation
Indices: 101434--101484 Score: 79
Period size: 3 Copynumber: 17.3 Consensus size: 3
101424 AAAAAAAGAG
101434 ATA ATAA ATA ATA AT- ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
101478 ATA ATA A
1 ATA ATA A
101485 GAGCATAGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.09
3 38 0.84
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:101462 original size:17 final size:18
Alignment explanation
Indices: 101434--101484 Score: 79
Period size: 17 Copynumber: 2.9 Consensus size: 18
101424 AAAAAAAGAG
101434 ATAATAAATAATAAT-ATA
1 ATAAT-AATAATAATAATA
101452 ATAATAATAATAATAAT-
1 ATAATAATAATAATAATA
101469 ATAATAATAATAATAA
1 ATAATAATAATAATAA
101485 GAGCATAGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
17 25 0.78
18 7 0.22
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
ATAATAATAATAATAATA
Found at i:101465 original size:20 final size:20
Alignment explanation
Indices: 101434--101484 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
101424 AAAAAAAGAG
101434 ATAATAAATAATAATATAATA
1 ATAAT-AATAATAATATAATA
101455 ATAATAATAATAATATAATA
1 ATAATAATAATAATATAATA
101475 ATAATAATAA
1 ATAATAATAA
101485 GAGCATAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 25 0.83
21 5 0.17
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAATAATAATAATATAATA
Found at i:103472 original size:15 final size:15
Alignment explanation
Indices: 103429--103473 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
103419 AATTTAAGAT
*
103429 TTTAATATTT-TTAA
1 TTTAATATTTATTTA
*
103443 ATTAA-ATTTATTTA
1 TTTAATATTTATTTA
103457 TTTAATATTTATTTA
1 TTTAATATTTATTTA
103472 TT
1 TT
103474 AATGATTATG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
13 4 0.15
14 11 0.42
15 11 0.42
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTAATATTTATTTA
Done.